The leading cause of death in HIV-infected individuals.
Weakened immune system
Limits sensitivity of diagnosis of TB
Support vector machine to find 251-gene signature
Our aim:
Explore genes with a significant expression enriched in HIV with TB co-infection
Compare with the 251-gene signature found with the SVM model
Keep it clean and tidy:
Select variables
Mutate variables
Handle key-variable
Handle replications
Normalization - minimize technical variability
Log transformation - stabilize variance, reduce skewness
Quantile Normalization:

Variance explained by the principal components
First PC explains 15% of the variance
31 PCs needed to explain 90% of variance
Scatter plot of projected observations onto PC1 and PC2
Slight division of disease state on PC1
No clear division of gender
Forest plot
Volcano plot